Simon J. Puglisi

Simon J. Puglisi always looks tired these days Simon J. Puglisi used to live way down south
[Simon J. Puglisi used to live way down South.]
Academy of Finland Fellow
Department of Computer Science
University of Helsinki
P. O. Box 68
(Pietari Kalmin katu 5)
email: puglisi [at] cs [.] helsinki [.] fi
office: A238, Kumpula Kampus
I'm an Associate Professor and Academy of Finland Fellow at the University of Helsinki in the Department of Computer Science. I lead the Compressed Data Structures group, and am a member of the Algorithmic Bioinformatics and the Practical Algorithms and Data Structures on Strings groups.

Prior to that I was a Newton Fellow in the Algorithms and Bioinformatics group at King's College London, and earlier still I held an Australian Postdoctoral Fellowship in the Search Engine Group at RMIT.

My current research focuses on efficient algorithms and data structures for searching, storing, and manipulating strings, trees and graphs, and applications thereof (like bioinformatics, information retrieval, database systems, and data mining).

I obtained my PhD from Curtin University, Western Australia, under the supervision of Bill Smyth and Andrew Turpin.

Selected (+ Recent) Publications

A fairly complete list is at DBLP. And then there is also Google Scholar.

Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, and Simon J. Puglisi. Fixed Block Compression Boosting in FM-Indexes: Theory and Practice, Algorithmica, to appear (2018).

Andrea Ferruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, and Jouni Siren. Relative Suffix Trees, The Computer Journal 61(5): 773-788 (2018).

Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Siren. Document retrieval on repetitive string collections, Information Retrieval Journal 20(3): 253-291 (2017).

Yasuo Tabei and Simon J. Puglisi. Scalable Similarity Search for Molecular Descriptors Proceedings of the 10th International Conference on Similarity Search and Applications (SISAP) (2017).

Juha Kärkkäinen, Marcin Piatowski, and Simon J. Puglisi. String Inference from Longest-Common-Prefix Arrays Proceedings of the 44th International Colloquium on Automata, Languages, and Programming (ICALP) (2017).

Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, and Arseny Shur. On the Size of Lempel-Ziv and Lyndon Factorizations, Proceedings of the 34th International Symposium on Theoretical Aspects of Computer Science (STACS) (2017).

Andrea Poyias, Simon J. Puglisi, and Rajeev Raman. Compact Dynamic Rewritable (CDRW) Arrays, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX) (2017).

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, and Bella Zhukova. Engineering External Memory Induced Suffix Sorting, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX) (2017).

Djamal Belazzougui and Simon J. Puglisi, Range Predecessor and Lempel-Ziv Parsing, Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA) (2016) [link to paper].

Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, and Simon J. Puglisi, Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices, Proceedings of the 22nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (2016).

Juha Kärkkäinen, Dominik Kempa, and Simon J. Puglisi, Parallel external memory suffix sorting, Proceedings of the 26th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS, 329-342 (2015) [code].

Martin Muggli, Simon J. Puglisi, Roy Ronen, and Christina Boucher, Misassembly detection using paired-end sequence reads and optical mapping data. Bioinformatics 31(12): 80-88 (2015).

Dominik Kempa and Simon J. Puglisi, Lempel-Ziv factorization: fast, simple, practical, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX), SIAM, 103-112 (2013) [link to paper][code].

Research Activities

I am Associate Editor at the ACM Journal of Experimental Algorithmics.
I am on the steering committee of SPIRE, the annual Symposium on String Processing and Information Retrieval.
I am on the steering committee of DSB, the annual Workshop on Data Structures for Bioinformatics.

I am on the programme committee for SPIRE 2020 and ALENEX 2021.

I was on the programme committee for WALCOM 2020, SEA 2020, FUN 2020, and ISMB 2020.
I was PC co-chair (with Nieves Brisaboa) of SPIRE 2019, held in beautiful Segovia, 7-10 October, 2019.
I was on the programme committee for CPM 2019.

I gave a keynote talk at SEA 2018, the 17th International Symposium on Experimental Algorithms, in L'Aquila, 27-29 June, 2018.
I was on the programme committee for ESA 2018, IWOCA 2018, and WALCOM 2018.
I organised (with Veli Mäkinen) the 4th Workshop on Data Structures on Bioinformatics, May 16-17, 2018. Here is a news item about it.

I organised (with Hideo Bannai and Yasuo Tabei) String Masters in Tokyo, October 13, 16, and 17, 2017.
I gave a keynote talk at PSC 2017, the annual Prague Stringology Conference, 28-30 August, 2017.
I was PC co-chair (with Rajeev Raman and Solon Pissis) of SEA 2017, held in wonderful London, June 21-23, 2017.

I was co-chair (with Yasuo Tabei) of WCTA 2016, which was a satellite to SPIRE in Japan.
I was PC co-chair (with Veli Mäkinen) of IWOCA 2016, which was held in Helsinki, August 17-19, 2016.
I gave a keynote talk at MatBio 2016, the 1st Conference on Mathematical Foundations of Bioinformatics, in London, July 20, 2016.

I was PC co-chair (with Emine Yilmaz and Costas Iliopoulos) of SPIRE 2015 in London in autumn 2015.
I was co-chair (with Costas Iliopoulos and Maxime Crochemore) of the Royal Society meeting on Storage and Indexing of Massive Data, February 7-8, 2013. Here is a group photo.
I was co-Chair (with Golnaz Badkobeh) of the organizing committee for LSD 2012.

I was on the programme committee for CPM 2017, IWOCA 2017, CIBB 2017, SPIRE 2017, SPIRE 2016, CPM 2015, IWOCA 2015, SEA 2014, SPIRE 2014, SEA 2013, IWOCA 2013, SPIRE 2012, IWOCA 2012, CPM 2011, IWOCA 2011, IWOCA 2010, CIKM 2009, and SPIRE 2008.
I was on the organizing committee for CPM 2012 and SPIRE 2008.
I occasionally review papers for the following venues.


Bella Zhukova (PhD, U. Helsinki, current)
Yan Zhengtong (PhD, U. Helsinki, current, co-supervied with Jiaheng Lu)
Pekka Jylha-Ollila (MSc, U. Helsinki, current)
Antti Karjalainen (MSc, U. Helsinki, current)
Lauri Heino (MSc, U. Helsinki, current)
Risto Haapasalmi (MSc, U. Helsinki, current)
Juusi Timmonen (MSc, U. Helsinki, current)
Joonas Nietosvaara (MSc, U. Helsinki, 2019)
Christopher Hoobin (PhD, RMIT, 2015, now at NASDAQ)
Jasbir Dhaliwal (PhD, RMIT, 2014, now at Monash U., formerly at IBM)
Alex Bowe (MSc, RMIT, 2013, now at Cruise Automation, PhD from U. Tokyo)
Shanika Kuruppu (PhD, U. Melbourne, 2013, now at Google)


I currently hold grants from the Academy of Finland, the National Science Foundation (NSF), and EU Horizon 2020.
I have held grants from the Royal Society, the Australian Research Council (ARC), and the Japan Society for the Promotion of Science (JSPS).

(recent) Teaching

I will run the Data Compression seminar course (website under construction) in spring 2019.
With Juha Kärkkäinen, I ran the Data Compression seminar course in spring 2017.
I looked after the Combinatorial Pattern Matching seminar course in autumn 2015.
With Travis Gagie, I taught Data Compression Techniques in spring 2015.
With Travis Gagie and Juha Kärkkäinen, I looked after the Advanced Data Structures seminar course in autumn 2014.


I try to travel overseas as much as possible.
I enjoy listening to Arvo Part, Colleen, Boards of Canada, and various other music.
I love reading.
Science on the Edge.
The Long Now Foundation.
The Saws by Robert Pinsky.
First Idyll by Susan Stewart.
Next Door and I Took Out the Part by Jessica Greenbaum.
Solitaire by Deborah Landau.
On Friendship by Hagit Grossman.